ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | (PHENIX.REFINE)精密化 | XDS | | データ削減 | SCALA | | データスケーリング | PHASER | | 位相決定 | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: PDB ENTRY 5G3P 解像度: 2.15→47.058 Å / SU ML: 0.21 / σ(F): 1.35 / 位相誤差: 19.67 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2021 | 5441 | 5 % |
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Rwork | 0.1786 | - | - |
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obs | 0.1793 | 108523 | 99.22 % |
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL |
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原子変位パラメータ | Biso mean: 45.41 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.15→47.058 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 13021 | 0 | 219 | 415 | 13655 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | 数 |
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X-RAY DIFFRACTION | f_bond_d0.003 | 14687 | X-RAY DIFFRACTION | f_angle_d0.625 | 20019 | X-RAY DIFFRACTION | f_dihedral_angle_d15.206 | 8822 | X-RAY DIFFRACTION | f_chiral_restr0.048 | 2086 | X-RAY DIFFRACTION | f_plane_restr0.005 | 2630 | | | | | |
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LS精密化 シェル | 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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2.15-2.1744 | 0.2601 | 179 | 0.2341 | 3423 | X-RAY DIFFRACTION | 100 | 2.1744-2.2 | 0.2676 | 172 | 0.238 | 3526 | X-RAY DIFFRACTION | 100 | 2.2-2.2268 | 0.2644 | 159 | 0.2281 | 3402 | X-RAY DIFFRACTION | 100 | 2.2268-2.255 | 0.2649 | 194 | 0.2301 | 3442 | X-RAY DIFFRACTION | 100 | 2.255-2.2847 | 0.2641 | 176 | 0.2245 | 3421 | X-RAY DIFFRACTION | 99 | 2.2847-2.316 | 0.2402 | 171 | 0.2085 | 3468 | X-RAY DIFFRACTION | 99 | 2.316-2.3491 | 0.2327 | 176 | 0.2032 | 3399 | X-RAY DIFFRACTION | 99 | 2.3491-2.3841 | 0.263 | 184 | 0.2072 | 3398 | X-RAY DIFFRACTION | 99 | 2.3841-2.4214 | 0.2141 | 153 | 0.1975 | 3433 | X-RAY DIFFRACTION | 99 | 2.4214-2.4611 | 0.2055 | 190 | 0.1972 | 3447 | X-RAY DIFFRACTION | 100 | 2.4611-2.5035 | 0.2158 | 188 | 0.193 | 3436 | X-RAY DIFFRACTION | 100 | 2.5035-2.5491 | 0.2036 | 192 | 0.1842 | 3428 | X-RAY DIFFRACTION | 100 | 2.5491-2.5981 | 0.211 | 190 | 0.1822 | 3437 | X-RAY DIFFRACTION | 100 | 2.5981-2.6511 | 0.2258 | 193 | 0.1827 | 3456 | X-RAY DIFFRACTION | 100 | 2.6511-2.7087 | 0.2194 | 214 | 0.1831 | 3402 | X-RAY DIFFRACTION | 100 | 2.7087-2.7718 | 0.2193 | 182 | 0.1769 | 3452 | X-RAY DIFFRACTION | 100 | 2.7718-2.8411 | 0.2087 | 176 | 0.17 | 3441 | X-RAY DIFFRACTION | 100 | 2.8411-2.9179 | 0.1943 | 186 | 0.1731 | 3454 | X-RAY DIFFRACTION | 100 | 2.9179-3.0037 | 0.1859 | 175 | 0.1739 | 3422 | X-RAY DIFFRACTION | 99 | 3.0037-3.1006 | 0.1919 | 200 | 0.1745 | 3412 | X-RAY DIFFRACTION | 99 | 3.1006-3.2114 | 0.2113 | 190 | 0.1771 | 3412 | X-RAY DIFFRACTION | 99 | 3.2114-3.34 | 0.1982 | 195 | 0.1718 | 3479 | X-RAY DIFFRACTION | 100 | 3.34-3.4919 | 0.1915 | 167 | 0.1643 | 3449 | X-RAY DIFFRACTION | 99 | 3.4919-3.676 | 0.198 | 197 | 0.1547 | 3410 | X-RAY DIFFRACTION | 99 | 3.676-3.9062 | 0.1771 | 169 | 0.152 | 3466 | X-RAY DIFFRACTION | 99 | 3.9062-4.2076 | 0.1686 | 169 | 0.1554 | 3438 | X-RAY DIFFRACTION | 99 | 4.2076-4.6307 | 0.1556 | 181 | 0.1377 | 3403 | X-RAY DIFFRACTION | 98 | 4.6307-5.3 | 0.1578 | 179 | 0.1473 | 3423 | X-RAY DIFFRACTION | 99 | 5.3-6.6744 | 0.1975 | 167 | 0.1856 | 3476 | X-RAY DIFFRACTION | 99 | 6.6744-47.0693 | 0.2201 | 177 | 0.1923 | 3427 | X-RAY DIFFRACTION | 96 |
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION ID | L11 (°2) | L12 (°2) | L13 (°2) | L22 (°2) | L23 (°2) | L33 (°2) | S11 (Å °) | S12 (Å °) | S13 (Å °) | S21 (Å °) | S22 (Å °) | S23 (Å °) | S31 (Å °) | S32 (Å °) | S33 (Å °) | T11 (Å2) | T12 (Å2) | T13 (Å2) | T22 (Å2) | T23 (Å2) | T33 (Å2) | Origin x (Å) | Origin y (Å) | Origin z (Å) |
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1 | 0.8636 | 0.1503 | 0.0229 | 2.6681 | 0.0995 | 2.552 | 0.1583 | 0.0387 | 0.1915 | -0.0196 | -0.2546 | -0.3219 | -0.0838 | 0.0952 | -0.0192 | 0.2485 | -0.0742 | 0.0084 | 0.2686 | -0.0294 | 0.2188 | 40.2684 | 6.4176 | 49.1718 | 2 | 4.598 | -3.8827 | 1.1243 | 5.8711 | -0.4977 | 1.5087 | 0.2268 | -0.44 | 0.3978 | 0.0189 | -0.0567 | -0.7222 | -0.0332 | 0.2262 | -0.019 | 0.3699 | -0.0848 | 0.0007 | 0.4488 | -0.0221 | 0.3394 | 45.4552 | 7.0429 | 57.7387 | 3 | 2.2289 | -0.1986 | 0.3374 | 2.5624 | -0.2679 | 1.5002 | 0.1125 | -0.2535 | -0.2724 | 0.2193 | -0.0683 | -0.0747 | 0.1535 | 0.0668 | -0.0317 | 0.3106 | -0.0861 | -0.0196 | 0.3503 | 0.0469 | 0.3019 | 38.7507 | -3.8065 | 54.6237 | 4 | 2.1922 | 0.5026 | 0.6592 | 1.3507 | -0.149 | 0.59 | 0.0823 | -0.0124 | -0.2307 | 0.0239 | -0.0081 | 0.0518 | 0.201 | -0.0815 | -0.0429 | 0.3371 | -0.063 | 0.002 | 0.358 | -0.0106 | 0.3638 | 29.1847 | -3.3496 | 42.3267 | 5 | 3.4686 | -0.0145 | 0.0674 | 0.5598 | -0.3261 | 0.6691 | 0.0169 | -0.005 | 0.1662 | -0.0121 | -0.0251 | 0.1588 | 0.0403 | -0.1086 | 0.0067 | 0.3259 | -0.0342 | -0.0001 | 0.3301 | -0.0327 | 0.3534 | 31.1019 | 7.2251 | 40.9317 | 6 | 4.3677 | -2.4282 | 0.6233 | 8.641 | 0.5815 | 4.6931 | 0.3046 | -0.0489 | -1.0006 | -0.5208 | -0.0457 | 0.1868 | 0.8128 | 0.1901 | -0.2008 | 0.5081 | -0.0951 | -0.018 | 0.4157 | 0.1283 | 0.4718 | 18.5051 | -19.3306 | 35.58 | 7 | 2.5458 | 0.2093 | 0.2027 | 3.0113 | 0.4273 | 2.1084 | 0.0234 | 0.7897 | 0.0881 | -0.4169 | 0.0457 | 0.1579 | -0.0201 | -0.1102 | -0.074 | 0.415 | 0.0718 | -0.0236 | 0.5812 | 0.0738 | 0.3221 | 26.6028 | 20.7234 | -10.4299 | 8 | 4.4111 | 0.2872 | 0.4793 | 5.5766 | 1.8524 | 3.3322 | 0.1051 | 0.8223 | -0.3378 | -0.0966 | 0.0016 | -0.2748 | 0.0541 | 0.4031 | -0.1316 | 0.343 | 0.0835 | 0.0574 | 0.6116 | 0.0253 | 0.3452 | 38.8732 | 17.0194 | -9.3402 | 9 | 2.2813 | 1.161 | 0.4193 | 0.5212 | 0.4302 | 0.6301 | 0.0956 | 0.088 | 0.0323 | -0.0359 | -0.0791 | -0.0854 | 0.0138 | 0.0963 | -0.0219 | 0.3429 | 0.0573 | 0.0232 | 0.4185 | 0.0387 | 0.3677 | 37.228 | 17.4455 | 4.8156 | 10 | 7.872 | -5.1666 | -3.2807 | 5.3234 | 1.7533 | 6.7069 | -0.2158 | 0.7888 | -0.8346 | -0.4287 | 0.1416 | -0.4156 | 0.3926 | 1.0547 | 0.069 | 0.3863 | 0.0026 | 0.101 | 0.6364 | 0.0311 | 0.3349 | 60.6125 | 7.3893 | -3.1215 | 11 | 1.5838 | -0.2797 | -0.9214 | 2.7646 | -1.2994 | 1.7351 | 0.041 | -0.4679 | 0.1958 | -0.0503 | -0.2631 | 0.2319 | -0.0646 | 0.0384 | 0.2468 | 0.3 | 0.0644 | 0.029 | 0.3162 | 0.0335 | 0.24 | 58.3075 | 4.0476 | 28.9192 | 12 | 5.1287 | 5.1332 | 1.7106 | 5.3484 | 0.7516 | 3.3675 | 0.2007 | -0.5773 | 0.0349 | 0.7321 | -0.3701 | -0.1509 | 0.0679 | 0.6124 | 0.2547 | 0.3926 | 0.0922 | -0.0088 | 0.4541 | 0.0541 | 0.3672 | 65.4798 | 0.8208 | 34.8129 | 13 | 1.9444 | 1.6081 | -0.4081 | 2.0571 | -0.7711 | 1.0648 | 0.1605 | -0.232 | 0.1544 | 0.0948 | -0.2588 | 0.2369 | 0.1166 | 0.298 | -0.0385 | 0.3579 | 0.0899 | 0.0347 | 0.3924 | 0.0171 | 0.3358 | 60.2217 | 2.6505 | 27.0073 | 14 | 3.9254 | 1.0505 | -0.1869 | 6.1136 | -0.5001 | 2.0681 | 0.1402 | -0.2066 | 0.4641 | 0.2993 | -0.1732 | -0.5877 | -0.0577 | 0.6495 | -0.0327 | 0.3899 | 0.0111 | 0.0296 | 0.5541 | 0.0243 | 0.4201 | 74.89 | 13.2133 | 25.3412 | 15 | 3.3361 | 1.8739 | -0.355 | 2.8593 | -0.3928 | 1.7753 | 0.0601 | -0.1837 | -0.467 | 0.0046 | -0.1553 | -0.5256 | 0.3557 | 0.4864 | 0.1004 | 0.3657 | 0.1078 | 0.0495 | 0.4688 | 0.0196 | 0.3886 | 67.3276 | -4.2961 | 25.9645 | 16 | 3.8393 | 1.754 | -0.9936 | 3.2043 | -0.6379 | 2.2824 | -0.1021 | 0.2642 | 0.2767 | -0.1771 | 0.1013 | -0.2227 | -0.1118 | 0.6623 | 0.062 | 0.3369 | 0.0658 | 0.0592 | 0.5781 | 0.0128 | 0.3888 | 73.6089 | 7.6752 | 16.9109 | 17 | 2.6241 | 0.9607 | 0.3067 | 4.6727 | -2.1293 | 3.5786 | -0.138 | -0.008 | 0.2302 | -0.1724 | -0.0329 | -0.3803 | -0.226 | 0.2689 | 0.2487 | 0.3365 | 0.0741 | 0.0201 | 0.4985 | -0.0251 | 0.3073 | 65.4537 | 7.3105 | 16.4233 | 18 | 2.4963 | 2.5507 | -0.8635 | 6.0941 | -1.4663 | 2.3839 | -0.0014 | 0.3715 | -0.4087 | -0.2376 | -0.0314 | -0.3272 | 0.3271 | 0.4044 | 0.2197 | 0.4092 | 0.1171 | 0.0656 | 0.492 | -0.0052 | 0.3338 | 62.312 | 0.5787 | 12.2508 | 19 | 1.7847 | 0.8491 | 0.3396 | 0.4452 | 0.0769 | 1.1956 | -0.1182 | 0.2134 | 0.0618 | -0.228 | 0.1822 | -0.1218 | -0.1075 | 0.2648 | -0.048 | 0.4006 | 0.0873 | 0.0395 | 0.4512 | -0.0061 | 0.3496 | 56.1395 | 7.7503 | 12.0275 | 20 | 2.6229 | 0.8776 | 1.2379 | 7.3977 | 5.2533 | 3.8771 | -0.0624 | 0.1108 | 0.2604 | 0.3536 | -0.0034 | 0.0473 | 0.2407 | -0.0434 | 0.0306 | 0.3797 | 0.049 | 0.0413 | 0.3953 | 0.0107 | 0.3558 | 46.9238 | 11.8054 | 15.687 | 21 | 1.1252 | -0.2339 | 0.4156 | 0.9853 | 0.7554 | 2.1721 | 0.0295 | 0.1501 | -0.0283 | -0.1757 | -0.1255 | 0.0089 | 0.1645 | -0.0571 | 0.083 | 0.3112 | 0.0218 | 0.0492 | 0.349 | 0.0228 | 0.2823 | 49.4137 | 6.3526 | 24.0738 | 22 | 4.3161 | 4.4172 | -3.772 | 5.1296 | -5.8349 | 9.0053 | -0.328 | 0.5101 | -0.0469 | -0.438 | 0.24 | -0.3344 | 0.2516 | -0.0988 | 0.032 | 0.3066 | 0.1339 | 0.1074 | 0.5059 | -0.0922 | 0.409 | 53.0119 | 5.7535 | -1.5948 | 23 | 2.126 | -0.0692 | -0.4549 | 1.5277 | 0.1565 | 2.741 | -0.0699 | -0.1895 | 0.4113 | 0.1895 | 0.0435 | -0.3622 | -0.2503 | 0.2357 | 0.0078 | 0.3078 | -0.0159 | -0.0411 | 0.2581 | -0.028 | 0.4644 | 52.589 | 36.1628 | 42.0606 | 24 | 4.4647 | -2.3404 | 0.885 | 1.3707 | 0.0405 | 2.261 | -0.403 | -0.4984 | -0.2003 | 0.407 | 0.5214 | 0.3372 | -0.4208 | -0.8434 | -0.1491 | 0.4654 | 0.0123 | 0.0223 | 0.4682 | -0.0512 | 0.483 | 35.7421 | 37.7506 | 46.9724 | 25 | 1.0093 | -1.0144 | 1.0875 | 1.6196 | -0.5992 | 1.1573 | 0.0447 | 0.0195 | 0.2227 | -0.0741 | -0.1164 | -0.0603 | -0.1308 | -0.0256 | 0.0855 | 0.3195 | 0.0078 | 0.0125 | 0.3013 | 0.0002 | 0.4201 | 38.8698 | 31.2964 | 31.0749 | 26 | 8.8025 | -1.7877 | -1.16 | 4.5442 | 1.1626 | 0.353 | -0.2432 | -0.8107 | 0.633 | -0.0071 | 0.1203 | 0.4109 | -0.7194 | -0.75 | -0.0398 | 0.5163 | 0.0637 | -0.0742 | 0.3174 | -0.0802 | 0.4839 | 17.7748 | 47.034 | 34.2185 | 27 | 1.2858 | 0.3165 | 0.504 | 2.1013 | -0.8856 | 2.5066 | -0.0658 | -0.0585 | 0.1442 | -0.0769 | -0.0741 | 0.4757 | -0.2083 | -0.3912 | 0.0976 | 0.3074 | 0.0337 | -0.0495 | 0.4323 | -0.0823 | 0.4753 | 1.1703 | 26.065 | 17.4588 | 28 | 3.5082 | 0.747 | 0.3663 | 5.5573 | -0.8872 | 6.1289 | -0.1325 | 0.0257 | 0.6225 | 0.0014 | -0.0583 | 0.1377 | -0.9215 | 0.065 | 0.2669 | 0.3597 | 0.1184 | -0.0879 | 0.3237 | -0.0775 | 0.4335 | 6.3026 | 38.7882 | 21.9825 | 29 | 0.6199 | -0.4376 | 0.7186 | 1.2195 | 0.46 | 2.4235 | -0.0446 | -0.0825 | 0.148 | 0.0758 | -0.0483 | 0.0666 | -0.0791 | -0.0818 | 0.0978 | 0.2998 | 0.0074 | -0.0174 | 0.3292 | -0.0572 | 0.3862 | 17.0118 | 25.8238 | 27.4301 | 30 | 4.6904 | -0.3524 | 1.1011 | 2.1579 | -2.5226 | 6.2644 | -0.1486 | -0.3589 | 0.5548 | 0.2827 | -0.0731 | 0.1125 | -0.6773 | -0.025 | 0.2256 | 0.5781 | 0.0804 | 0.0304 | 0.4208 | -0.1252 | 0.4501 | 25.577 | 46.9568 | 37.714 | 31 | 1.4637 | 1.7539 | -1.1074 | 3.3277 | 0.4871 | 3.7185 | -0.3176 | 0.043 | 0.7266 | 0.0099 | 0.2164 | -0.0389 | 0.1378 | -0.1791 | 0.0535 | 0.4322 | -0.0049 | -0.1072 | 0.2882 | -0.0384 | 0.2486 | 15.5538 | -2.5859 | 9.2318 | 32 | 8.7786 | -0.7704 | -1.8675 | 1.0845 | 0.148 | 3.1623 | 0.0553 | 0.6194 | 0.4611 | -0.3793 | 0.0722 | 0.2376 | 0.0838 | -0.3667 | -0.1883 | 0.5794 | 0.0027 | -0.1253 | 0.4618 | -0.0441 | 0.404 | 10.2061 | -5.2802 | 1.2388 | 33 | 3.8422 | 0.1624 | -0.4828 | 1.4308 | -0.3545 | 2.7075 | 0.1729 | 0.1518 | -0.3257 | -0.2589 | 0.0479 | 0.1868 | 0.4496 | -0.3655 | -0.1508 | 0.4777 | -0.0699 | -0.1518 | 0.3692 | 0.0129 | 0.3726 | 8.863 | -10.0152 | 8.9077 | 34 | 6.7472 | -2.0116 | -2.5009 | 2.5748 | 0.2596 | 6.1064 | 0.121 | -0.0523 | -0.7567 | -0.1059 | -0.0772 | 0.33 | 0.5813 | -0.3884 | 0.0413 | 0.5439 | -0.1279 | -0.2025 | 0.2988 | -0.0067 | 0.466 | 9.3104 | -17.8209 | 14.5644 | 35 | 8.8104 | -1.8053 | -1.3255 | 3.4268 | -1.0141 | 6.2386 | -0.2711 | -1.134 | 0.151 | 0.726 | 0.5987 | 0.3753 | -0.1505 | -0.782 | -0.3427 | 0.4517 | -0.0002 | -0.0944 | 0.6033 | -0.0028 | 0.4136 | 7.0238 | -9.4314 | 26.009 | 36 | 1.4985 | -0.8667 | 0.726 | 1.5602 | -0.9969 | 0.4219 | 0.065 | -0.008 | -0.0351 | -0.0866 | -0.017 | 0.0263 | 0.1874 | -0.0759 | -0.0124 | 0.4069 | -0.0078 | -0.0505 | 0.3429 | -0.0162 | 0.3413 | 21.34 | -3.6748 | 21.0465 | 37 | 2.3632 | -1.2285 | 0.6221 | 2.8872 | -1.0378 | 1.3731 | 0.3122 | 0.2687 | -0.0764 | -0.4193 | -0.3401 | -0.2274 | 0.5138 | 0.1056 | 0.0942 | 0.468 | 0.0338 | -0.0023 | 0.4345 | 0.0008 | 0.453 | 34.2741 | -11.6461 | 16.2223 | 38 | 9.3264 | 0.3584 | -4.037 | 5.6861 | -0.5516 | 2.3087 | 0.1059 | -0.5526 | -0.4095 | 0.9727 | 0.1581 | 0.0842 | 0.475 | 0.0804 | -0.2446 | 0.5945 | -0.108 | -0.1582 | 0.4668 | 0.0557 | 0.5463 | 21.253 | -16.8318 | 41.9637 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details |
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1 | X-RAY DIFFRACTION | 1 | CHAIN 'A' AND (RESID 12 THROUGH 28 )2 | X-RAY DIFFRACTION | 2 | CHAIN 'A' AND (RESID 29 THROUGH 49 )3 | X-RAY DIFFRACTION | 3 | CHAIN 'A' AND (RESID 50 THROUGH 141 )4 | X-RAY DIFFRACTION | 4 | CHAIN 'A' AND (RESID 142 THROUGH 210 )5 | X-RAY DIFFRACTION | 5 | CHAIN 'A' AND (RESID 211 THROUGH 267 )6 | X-RAY DIFFRACTION | 6 | CHAIN 'A' AND (RESID 268 THROUGH 308 )7 | X-RAY DIFFRACTION | 7 | CHAIN 'B' AND (RESID 12 THROUGH 120 )8 | X-RAY DIFFRACTION | 8 | CHAIN 'B' AND (RESID 121 THROUGH 163 )9 | X-RAY DIFFRACTION | 9 | CHAIN 'B' AND (RESID 164 THROUGH 267 )10 | X-RAY DIFFRACTION | 10 | CHAIN 'B' AND (RESID 268 THROUGH 307 )11 | X-RAY DIFFRACTION | 11 | CHAIN 'C' AND (RESID 12 THROUGH 28 )12 | X-RAY DIFFRACTION | 12 | CHAIN 'C' AND (RESID 29 THROUGH 49 )13 | X-RAY DIFFRACTION | 13 | CHAIN 'C' AND (RESID 50 THROUGH 67 )14 | X-RAY DIFFRACTION | 14 | CHAIN 'C' AND (RESID 68 THROUGH 82 )15 | X-RAY DIFFRACTION | 15 | CHAIN 'C' AND (RESID 83 THROUGH 105 )16 | X-RAY DIFFRACTION | 16 | CHAIN 'C' | | | | | | | | | | | | | | | |
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